Metroid: Fugitive
by Brennan4
Summary: In this sequel to Fusion, Samus and Adam find themselves on the run from the Federation following the events on B.S.L. They must fight a looming conspiracy, the rising Space Pirate forces, and other malevolent enemies.  COMPLETE!
1. Prologue

Author's Notes: Hello!This is my first fanfic, so please keep that in mind. That said, this is probably going to go on for some time, so expect it to improve towards the end.

Samus was starting to feel more like herself again. Maybe that was because the stress was starting to die down, or maybe it was because absorbing the SA-X had started to neutralize the metroid part of her. It had been a few hours since the destruction of B.S.L., and she was traveling with Adam, Dachora, and the Etecoons.

"**I have detected a nearby Federation vessel,"** said Adam. **"They appear to be trying to send us a message. "**

Samus turned on the ship's communicator. This was it. They would either accept her story, or she would be fully prosecuted for the damages she had inflicted. She listened to the incoming message.

"Attention Samus Aran. You are under arrest for destruction of Galactic Federation property and the planet SR388."

The next thing she knew, Samus was waiting in a cell on the Federation ship. They had deactivated her power suit, stored Adam to an external drive, and sent Dachora and the Etecoons to a quarantine lab. She had been waiting for what felt like hours, growing increasing frustrated. She knew a long line of red tape was ahead of her, and she didn't know if she could get through it without getting stuck.

She saw she had a visitor. A lean, if slightly ungainly figure in black and green armor approached. She recognized him as Algor, largely considered to be one of the greatest bounty hunters in the galaxy, next to herself, of course. Samus and Algor had always had a bit of a rivalry ever since he missed the opportunity to participate in the Aurora Unit incident. She noticed his armor resembled her own, even more than the last time she saw him. She had always suspected he was trying to reverse-engineer some of her capabilities in order to augment his own strength.

"Well Samus, you've really done it this time. The other bounty hunters are usually willing to ignore your habit of planetary destruction, provided it actually benefits you assignment. What were you thinking? This is going to seriously damage the already controversial bounty hunter occupation.

Samus remained silent, a common response during periods of high stress and anger. She listened to him rant, pretending he wasn't absolutely enjoying this. He wasn't an evil person, like some of their other associates, but he was certainly one of the more irritating individuals in the profession.

She waited for a little while until he left, satisfied he was not going to get a response out of her. She heard a quiet beeping on her wrist communicator. _That's odd, _she thought to herself. Her loner nature meant she didn't have anyone to bail her out, not that the Federation would let her out anyway.

"**How are you doing, Lady?"** chimed the now familiar voice of Adam. **"Be prepared, I am now going to reactivate your power suit. I'm afraid I had to use the file before the B.S.L. incident, so your weapon upgrades are no longer activated."**

_Figures,_ she thought to herself. Her weapon capabilities had a habit of being disabled between missions. Her body shimmered as her blue and yellow Fusion suit materialized. "How did you contact me? What's the plan?" she asked.

"**I was able to hack my way out of the storage unit and wirelessly transport myself to your communicator. We'll be able to stay in touch at all times. **

_Great, _she thought to herself. She had grown tired of him over the past day, helpful as he was.

"**I intercepted some troubling chatter while they were transporting me. It seems certain forces in the Federation have no plan of giving you a fair trial, and plan to cover up the experiments. I determined the best course of action would be to release you and assist you in building a case against them. Any objections, Lady?"**

"Hell no," replied Samus. "Let's get out of here." She blasted through the cell door, and began running as the alarm klaxons blazed. She saw a pair of Federation guards ahead of her. No slowing for a second, she jumped in the air and delivered a spin kick to both of them at once, knocking them out. She saw another platoon of 3 guards, running at her with their stun pistols drawn. She dodged their fire and returned a volley of warning shots in a strafing maneuver. While they took cover from her shots, she jumped over a barrier and ran off, leaving them unable to catch her.

As she made her way to the hangar, she asked Adam, "Where should we go?" He replied, **"I heard mention of a planet called Espan XI. In addition to a moderately successful colony, there are some Chozo ruins. They may help you regain your abilities, and resist the Federation."**

I seemed as good a plan as any, given their options. She jumped into the cockpit of her ship, which was being transported to be impounded, and took off. Adam set a course for Espan XI. She was now officially a fugitive. Algor, this rogue faction in the Federation, and half the Federation itself would shortly be pursuing her, and she was once again at limited capability. Given what she had been through the previous day, she didn't fell too troubled by that.

**To be Continued**

Author's Note: Well, I hope you enjoyed that. I will try to get at least one full chapter up before I leave for the holiday, then a few more when I get back. Please review, any praise or criticism is greatly appreciated, and will help improve the quality of the story. Hope to see you again soon. 


	2. Chapter 1: Chozo Ruins

Author's Note: Alright, here's where the story really gets started. This chapter is meant to mirror the opening level of Super Metroid or Zero mission, so it may be a little light on plot. 

They landed in an open field. Samus hopped out of the ship, and descended down a shaft into a network of caves. Like Zebes, the ruins on this planet were located primarily underground. She started to inspect the statues, until at last she found what she was looking for. In the cupped hands of one of the statue was a small glowing orb. The fired a small shot at it. As the orb shattered, a faint glow of energy passed into her.

"**My scans indicate you have just recovered the morph ball ability," **said Adam. Now Samus would be able to curl into a ball and access smaller places. She used this new ability to travel through a small cavern and continued onwards. She noticed the caves were infested with Zoomers, Skrees, and other hostile life forms. She was usually able to pass by or destroy these creatures, but they made things slightly more challenging.

She walked and climbed her way through the caves until she found another small crevice. As she morphed and rolled into it, she found it had been blocked off by small rocks that she could not budge out of place. She rolled back out, but knew exactly how to proceed.

"The Chozo designed their training around the escalation of one's skills and abilities," she explained to Adam. "In order to continue, I will have to locate the Bomb data and use that to progress."

A little more exploration led her to another statue with an orb in its hands. This one did contain the upgrade she was looking for. Now, while in ball form, she could lay bombs for offensive and exploratory purposes. She returned to the crevice and passed through with ease. She continued to navigate, searching for the next essential weapons, missiles and the Charge Beam.

She entered a section of the temple that was crawling with wildlife, yet all of the creatures seemed to be hiding or burrowing. She looked ahead and saw a pair of robots, which she recognized as of Federation design. One of them droned, in a monotone voice, "Samus Aran. You are under arrest. You have been officially declared a fugitive, considered armed and dangerous. Deadly force has been authorized if you do not comply."

She went into a defensive stance, making it quite clear she had no intention of coming quietly. As the robots opened fire, she used her morph ball ability to dodge out of the way. She rolled up onto a wall, bouncing behind them. She resumed her normal form and shot them both in the back, blowing their heads clean off.

"**Hold on a moment," **said Adam. **"I think I may be able to intercept Federation communications. This could provide valuable information about our adversaries."** After a few moments, they heard a slightly garbled transmission. Two voices were easily heard, a gruff and agitated on and a noticeably calmer, more restrained one.

"Units 342 and 534 please respond," said the first. He continued, "Have you encountered the fugitive yet?"

Samus replied, "That's one way of putting it. Who do I have the pleasure of speaking to?"

The first voice answered, "I am Commander Graeme, and this is Colonel Wicket. I am the chief officer of the Scientific Oversight Committee. The B.S.L. station was my pet project, and you blew that up, which is why I am leading the manhunt to arrest you." Graeme continued, "I was also heavily involved in the Bottle Ship Lab, which you also destroyed. That's why this is personal."

Wicket chimed in, "Listen Samus, I've read the file and you might have a case in your favor. Come quietly and we might be able to work this out."

"It'll take more than your weak good-cop/bad-cop routine to bring me in. I know you're trying to rig the trial. The moment I turn myself in, my freedom and the truth about what happened on that station both die." said Samus. With that, she jumped away and continued on her trek.

After a little while she came to a large, cylindrical shaped cave. There were a few different passageways, so she took the one closest to her first. It turned out to be a dead end, but she found a missile tank at the end. At last she would be able to utilize her most tactical weapon. As she returned to the cave, she noticed it a rumbling noise. Some rocks were shaken loose and bounced around the walls and onto the floor.

An enormous, centipede- like creature burrowed out of the ceiling and between the walls, blocking off the exits with its gigantic, spiky body. She recognized the creature, known as Deorem, having faced one on Zebes. It opened its single, bloodshot eye, and clamped its pincers with anticipation.

Samus tried to fire at its eyeball, the only part of its body she could hurt. But it closed its armored eyelid, blocking her shots. While she waited to fire again, she felt sharp pricks in various points on her body. The creature was launching the spikes on its body at her as projectiles.

As she dodged the spike, the creature opened its eye and rammed her into the ground. As she got up she fired some of her newly gained missiles, hitting it in its eye. The creature became clearly agitated, increasing the frequency of the attacks. Its body pulsated at a higher rate as a result of its pain and anger.

The Deorem came back down for a second strike, but Samus was able to avoid it by morphing. It snapped its pincers angrily, trying to grasp the little ball. She laid a bomb which hurt the beast, further frustrating it. Blinded by pain, it weaved its head in the air, and knocked Samus against a wall.

It approached her to deliver the final blow. Samus unloaded as many missiles as she could, each one hitting it squarely in its enormous eye. The creature shrieked as its body segments shook and exploded. Samus approached the creatures head, and noticed a strange feeling in her hand. Small spikes emerged from the center of her palm. They were similar in shape to the mandibles of a metroid.

For a reason she could not quite understand, she felt compelled to touch the creatures head. As the spikes attached to the head, she felt a strong wave of energy move through her. **"You seem to have recovered the charge beam."** said Adam. Samus asked, "How is that possible?" Adam answered, **"My best guess is this is another ability granted to you by the metroid vaccine. You can absorb strength from any life form, not just the X parasite."**

_I don't know whether to be horrified or excited about this, _Samus thought to herself. Absorbing the X had been strange, but this might be pushing it too far. She exited the cave. She had obtained all of the gifts the temples had to offer. She came out into a jungle area, teeming with life. Whatever she was becoming might just be enough to accomplish this mission.

Author's Note: Hope you enjoyed that. The next chapter may take a lttle while, but hopefully it will be worth it. There will be monsters, thrills, suspense, and a certain boss from Super Metroid will return. Please review! Any input is helpful. 


	3. Chapter 2: The Jungle

Author's Note: Well, I'm finally back. The next chapter is already written and should be uploaded shortly after some minor updates.

Samus took a moment to appreciate the lush environment before her. Every organism seemed to be vibrating together in the music of nature. Every time she found herself isolated like this, trapped on an unknown world with against unstoppable odds, , she always found comfort in exploring and admiring the world. As she soon found out, however, the wildlife was as hostile here as it had been in the caves. Creatures soared in the air and climbed through the trees, all seeing her as a threat.

"**We should be careful**." said Adam.** "Not only is the wildlife deadly, but the Federation manhunt is surely combing the jungle." **Samus leaped up into the trees and traveled by hopping and climbing among the branches. To her surprise, she discovered some of the branches were actually snake like-organisms, which caught her off guard a few times by wriggling and writhing around. Dragonflies with dozens of eyes and spider-like creatures that resembled hands were among the obstacles she faced. A rather cute monkey-like creature also seemed to view her as a threat, but she tried to avoid startling them.

After a while, she heard voices from below. "Are those what I think they are?" she asked Adam.** "If by that you mean Federation troops, I think the answer is yes. We should keep out of their way. Remember, they have authorized deadly force against you. " **he replied. "I'm almost flattered." deadpanned Samus. "In all seriousness, though, I have a better plan."

She jumped between branches, periodically firing off shots in the other direction. This grabbed the attention of both the search party and the wildlife. As Samus hoped, they kept each other busy and unfocused on her. Eventually, she was satisfied with the distance she had placed between them.

"Alright, where should I go now?" she asked Adam.

"**My best suggestion is would be a thermal vent, an industrial-looking cylindrical structure. Through it we can enter the colony's main reactor and infiltrate the facility. This is the last maneuver they would expect from us." **

Soon Samus found the structure and hopped on to a catwalk along the side. She began to scale it, eventually reaching the top. As she looked down, she saw long shaft lead to a bubbling cesspool of orange liquid."That would b fuel gel." explained Adam. "the colonist let it through here to vent off excess heat."

"Does this mean I'll be travelling through yet another ultra-temperature area without the benefit if my Varia Suit?" asked Samus.** "All signs point to an affirmative answer." **said Adam.

Samus slid down the inside of the structure, stopping on a worker's platform. She saw a large catwalk in the centers, suspended by pistons over the burning lake below. She stepped onto it, and cut through the mist that obscured her view. She walked up to some controls and activated them, and the platform began to descend into the lower levels of the reactor. From here she would be able to progress further into the colony.

Suddenly, a long, bony red arm sliced through the steam and its talons slashed her. The force of the attack threw her across the catwalk. She almost fell of the other side and into the burning liquid below. A familiar, honking growl sounded as a large, squat figure emerged into sight. It was round, with mushy skin, thin and bony appendages, and five eyes along each side of its crocodilian snout.

_Crocomire, _Samus thought to herself. _How could I have missed him? What's he even doing here? _Her thoughts were interrupted as a stream of fireballs hurtled towards her. She dodged out of the way, and saw Crocomire emerge and make a few steps towards her. _If he gets to close, he could push me off the ledge, _she thought. She launched a missile into his open mouth and he scuttled back instinctively, momentarily distracted by pain.

He unleashed another volley of fireballs and advanced towards her again. Samus could feel she was being pushed towards the edge, and into a fiery grave. She started and offensive strategy. Every time he opened his maw, Samus shot everything she had into his vulnerable throat, pushing him back. The fight became an inverted tug of war game, with each side trying to push the other back.

As Crocomire came closer to the edge, he took a more defensive stance. He spewed fireballs directly in front of him, using them as a sort of shield. As they rained down, Samus had to sneak close to him to continue hitting him back. She was greeted with another swipe of his arm, which flung her across the platform. She saw the awkward dragon start to move closer. All of her work was about to be undone, and he would again have the advantage. She dodged his next stream of fireballs and rolled out of the way of his arms. She jumped up into the air, looked Crocomire right in his various eyes, and launched a fully charged shot into the back of his throat. The impact pushed back into the flaming depths, and he began to dissolve almost immediately. Its bones were all that survived, floating in the gel.

Samus hopped across the bones and safely reached a service hatch on the inside. Something always disturbed her about the first Crocomire fight, and while this brought back the same sickening features, it raised a new question. What was a Space Pirate Lieutenant doing here? As she entered a service passway, Adam indicated a container on the wall. **"That's an emergency dispenser of cryogel, which the workers use to patch leaks and flooding. If you absorb it, you may be able to reactivate your Ice Beam ability." **Samus put her pal on the container and the spikes emerged, sucking out the gel. After a painful and intense wave of cold swept through her, she regained the Ice Beam.

Although she was now slightly stronger, she was still at a serious disadvantage against the odds that she would fail. Questions plagued her like buzzing flies in her head. What was the extent of the conspiracy against her? How widespread was the manhunt for her? And how were the Space Pirates involved? Feeling two steps behind, she descended into the burning corridors.

Author's Note: Sorry about the delay, the next chapter should be up shortly. Next time, Samus fights another bounty hunter and an old boss with a new twist. 


	4. Chapter 3: Interior Reactor

Author's note: How's that for a quick update! Don't get used to it; I probably won't be able to work this fast again anytime soon. Anyway, enjoy!

Samus could detect the heat even through her power suit. The walls almost seemed to shimmer and vibrate together. The area was clearly not meant for people without protective gear, yet here she was. However, she found something relaxing about it. Perhaps she had gotten used to areas like this or maybe the metroid part of her enjoyed shelter from cold air. Samus walked down the corridors, her boots making a _click-clack _noise on the metal floor. The hallways had an orange glow to them.

"**I am detecting nearby bio-signs. We should be cautious." **said Adam.

Just as he finished speaking, Samus heard several shots fire in rapid succession. She dodged a hail of incoming blasts, jumping back and forth between the shots like a dancer. She looked up and saw Algor, his two wrist-mounted cannons smoking. Samus knew she wasn't yet strong enough to fight him, so she decided to give him a chase.

As she ran, she heard him yell, "Stop where you are. The Federation is prepared to give you a bargain if you come with me. You'll want to hear what it is." In spite of herself, Samus turned around for a split second to listen to him. She was greeted with a series of rapid fire shots for doing so. _Clever little snake, _she thought.

She was able to dodge most of his shots, and her armor held up against the rest. She charged up a shot with her newly acquired Ice Beam and aimed at Algor. She froze him where he stood and continued running. She could hear him already beginning to thaw behind her. **"Quickly Samus, through here!" **said Adam, indicating a nearby air vent. Samus shot off the grate and morphed into a ball and rolled inside.

Behind her, she heard Algor yell, "This isn't over Samus! General Graeme has just authorized an artificial intelligence unit for me, so you won't be able to rely on your friend to get you out of this!" Although this did somewhat worry Samus, she took some small delight in knowing he, as always, was planning to copy her new abilities to make himself more formidable.

Samus came out of the other side of the vent. She resumed her normal form and took a moment to catch her breath. She heard a strange series of vibrations from her communicator, and asked Adam what was going on. He replied, in a more relaxed, lass authoritative voice, **"I think I'm beginning to recover some memories from my formers self. I just relived an incident when I lead an attack on a Space pirate outpost formed from the remains of a colony they destroyed. I remember thinking stopping them was a fruitless endeavor because we had already lost the people we came to save."**

Samus felt a twang of pity for Adam. She remembered hearing about the incident from the original Adam Malkovich, who was clearly bothered on a deep level by what had happened. From this computer she again detected a little a more human side which she had caught a glimpse of towards the end of the incident on B.S.L.

After a few moments, Adam seemed to have composed himself. **"I think I may have found a way out of here, but you will have to travel through an ultra-heated area to reach your destination. You need to reactivate your Varia Suit to proceed." **he said. Samus began searching the facility, her progress impeded by several heated rooms to dangerous for her to proceed through. Eventually she found a large room with several scaffolding platforms overlooking a large vat of fuel gel.

The gel began to bubble. Out of the fluid emerged a colossal, green, three-eyed reptile. Samus immediately recognized the form of Kraid even through the layer of steam concealing him. _So it wasn't random chance meeting Crocomire, _thought Samus. The Space Pirates really were up to something on Espan XI. As the steam began to clear, Samus saw that Kraid looked different from their previous encounters on Zebes. He had ben given cybernetic enhancements, most notably a large protective headgear. He resembled Meta-Ridley in his this way.

Meta-Kraid, as Samus now thought of him, roared and started his typical attacks. A seemingly unending stream of claws and spikes were fired, regenerated, and fired again. Samus was fast on her feet and sidestepped the organic projectiles with ease. However, Meta-Kraid did something unexpected. He opened his mouth and fires a beam of crimson energy. This struck Samus directly, and made her feel like she was being roasted alive. As Samus began to recover, another wave of spikes and claws began heading her way. Unable to avoid them, Samus simply did her best to endure the onslaught.

As meta-Kraid began to charge up his energy beam again, Samus fired her Ice Beam and froze his mouth wide open. Using the precious little time she had before he thawed, she fired as many missiles as she could at his head.

This caused the headgear to crack, but it still remained intact. The behemoth roared in anger. He demolished the platform that Samus was standing on. As she fell, Samus bounced off the wall and continued shooting. The three-eyed reptile launched spikes of her, one of which Samus froze in midair and rested upon. She then continued with on offensive barrage.

Meta-Kraid was now becoming visibly enraged at his elusive and resilient adversary. He charged and fired another beam blast. It missed Samus, but vaporized most of the spike she was standing on. This last attack proved a fatal mistake on the lizard's part. Samus again froze his head and fired at it until it shattered. The creature squealed as it sank into the vat of fuel gel.

Samus looked around the room and found a console used by the workers to generate protective bodysuits. From it she was able to download the Varia suit upgrade, which gave mild protection, less than it normally would. As such, her suit retained its standard coloration. Samus continued through the reactor, going through now accessible heated rooms. Adam asked her to pause at a steamy entrance hatch.

He explained, **"I have detected some highly encrypted communications from the Federation that may be of use to us. I cannot decode it while the colony mainframe A.I. is online. Right there is an entrance to the A.I. Central processor. It is probably heavily guarded. Is your objective clear?'**

Samus didn't hesitate to reply "Yes."

To be Continued


	5. Chapter 4: The Mainframe

Author's Notes: Sorry this one took so long. I've been pretty busy, so the next one will probably take a while too. Anyway, enjoy this chapter, in which Samus battles an insane computer. Trust me, it's more creative than it sounds.

Colonel Wicket carefully stepped into the Command Center of the Espan XI colony. This room was currently being used by the investigative team hunting Samus Aran. General Graeme was filling out some forms and occasionally muttering into his communicator. As always, he was handling stress poorly, and Wicket knew firsthand how volatile he could be at these times. That is why it was going to be so hard saying what he needed to say.

He finally worked up the courage to explain his findings. "Excuse me, general, but I have some new information for you. It is from the final transcripts from B.S.L. before we lost contact." He said quickly, his words practically tripping over each other. Graeme got up and looked directly at him, never seeming to blink.

Wicket continued, "It seems that several of the research projects were highly questionable and unstable. Samus may have done the Federation a great favor, saving countless lives. If we try a more diplomatic approach, we may get her in court to explain her side of the story."

Graeme gave an exasperated sigh and said, "If Samus wanted to talk, she's had plenty of opportunity to do so. Besides, whatever may have been happening on the station, Samus had no authority to justify her actions. A Federation team could have arrived in minutes before the lab's demolition. Now get back to work."

Samus stepped into the small, glowing hallway and immediately felt a rush of cold air, intensified by the heat of the room she had just left. The corridors were cramped, but uniquely detailed. Circuitry ran along the walls, and small lights would periodically flash and flicker. She asked Adam, "So, what exactly is the plan here?" She did her best not to shiver as she spoke.

"**This unit is one of the experimental S.E.I. systems, designed to run a colony and interact with the inhabitants on a more personal level." **replied Adam. **"The system has three distinct personalities, based on certain aspects of psychology. There is a "mother' personality, who is calm and restrained, a "father" personality who is authoritative and aggressive, and a "son" personality. This last one was intended to be carefree and exuberant, but the results were often deemed too chaotic."**

"**In order to disable the system, you will have to reach the processing core. There you must sabotage three processors, shutting off the personalities one by one.* SDRFFSDGdsXXFSDF13131*"**

Adam's last sentence deteriorated into a garbled mess of phonetic sounds and static before he eventually shut out. Samus was alarmed, desperately trying to raise him on the communicator, which was unresponsive. She heard a soft, feminine voice from some microphones in the walls.

"**I'm sorry, but you have accessed an unauthorized area. Please leave immediately, or deadly force will be used. And have a lovely afternoon!"** said the MOM personality. Something about it was truly disconcerting, as if the cheerfulness sounded unnecessarily genuine.

A number of orange, translucent force field appeared in the halls, and began rushing towards Samus. They followed simple geometric patterns, having sharp spikes or blunt, crushing surfaces. Samus ducked and weaved her way through the obstacles. She jumped on top of one as it advanced towards her, then ducked as a knife like prism swung above her, like a deadly game of limbo. She rolled, spun, and hopped between the orange blocks, finally reaching the end of the hallway.

"**Halt! Just what do you think you're doing here?" **said a second voice. This one was shrill and grating, the DAD personality. **"You are in violation of sections three, nine, and forty-seven of the colony policy contract!"** yelled DAD. Samus noticed two rocket sentries o the walls had taken note of her, and began firing.

"**This is what happens when you don't follow the rules!" **screamed DAD over the sound of the rockets. Despite his aggressive enthusiasm, Samus was able to easily blow apart the sentries and continue on her way. She came to a dark vent shaft with some caution tape over it. She saw from her visors ma system that it would lead to her destination, and crawled through it.

As soon as she reached a more roomy part of the shaft, a loud, cheery voice, SON, rang throughout the halls. **"Surprise!"** it shouted, dripping with glee.

Samus looked around and saw she was surrounded by security robots. **I brought some friends for you to play with."** SON snickered. Small, spider-like robots crawled on the walls. Floating drones with glowing photoreceptors and guided missile launches buzzed above the ground. Some more anthropomorphic-looking androids leveled assault rifles at her. A miniaturized version of the B.O.X. scuttled back and forth.

On the latter robot Samus thought, _Boy does he redefine the word "crabby",_ wishing she had thought of that joke on B.S.L. Bad puns were not going to get her out of this, so she blind fired with her Power Beam. As the robots temporarily backed off, she sped down the corridors.

Running as fast as she could, Samus had trouble checking her map and orienting herself. As such, she soon found herself backed in a corner. The mechanized forces surrounded her, weapons ready to fire. She beat them to it, launching Missiles rapid-fire in all directions. After a series of loud explosions, her path was cleared.

She traversed the cold, hi-tech labyrinth, following the objective Adam had marked on her map before he blinked out. She hoped he wasn't in pain and would be able to return once she shut off the A.I. she came to a bridge overlooking electrified fluid. She saw she was near the exit of the mainframe, and was adjacent to the core. Suddenly, the bridge began to retract.

She jumped up in the air, hoping to buy herself a few more seconds before she fell. To her surprise, she landed on one of the force field blocks, which was acting as a platform. A series of these appeared, leading her on a path to her objective.

"**Do you have any idea how much trouble you're in?" **said Dad, brimming with rage. **"Nobody in the history of this colony has broken as many regulations as you did today!" **__The more reassuring voice of MOM added, **"Why don't you come in here for a little chat?"**

With a slight sense of dread, Samus hopped over the platforms. She heard SON cheer, **"We're going to have so much fun!"**

Samus entered a large, glowing green room. A large, snakelike mechanical body was suspended from the ceiling, robed in wire. A three-eyed head, shining a brilliant shade of emerald, looked at her. MOM said, **"I'm afraid this may hurt a little bit." **A blur of orange sped into Samus, knocking her against a wall.

As she got up, she saw a barrage of the force field blocks coming towards her, and opened fire. Most of the shots ricocheted of the blocks, several hitting the A.I. right in its head. One of the eyes shattered, and the other two repositioned themselves. They now took on a scarlet hue, as did the room.

"**You just made the biggest mistake of your life!" **shrieked DAD. A number of mechanical arms emerged from the ceiling, all ending in rotating saw blades. They sliced at Samus tearing gashes in her Chozo Armor. Not able to take too much more punishment, she fired her Ice Beam, freezing them in place. Then she fired a Missile at the head, shattering another eye. The last eye repositioned itself. It began to flicker a myriad of colors, and a manic giggling sound filled the room.

"**Looks like it's just you and me now!"** squealed SON. Samus saw a cannon appear from inside the robotic body. It began firing small grenades in all directions. Samus never had more difficulty concentrating in a battle than right now. As SON began singing nursery rhymes, the room felt like a demented cross between a nightclub and a preschool classroom.

Samus did her best to avoid the bombs, but one exploded near her and knocked her on her back. The A.I took a second to glare at her, its final eye resembling a strobe light. She blasted a fully charged shot directly into it. A series of explosions and electrical sparks traveled through its body, which became still and silent.

Samus heard a buzzing on her communicator. **"Did you miss me Samus?"** asked Adam. Samus couldn't help but admit she had. **"Maybe I'm starting to remind you of the old Adam?" **

Samus said jokingly, "No, although anything but those three is an improvement." Adam didn't pick up on her tone, saying, **"Good, because I'm recovering some more memories, and you two seemed to have a fairly dysfunctional relationship. Anyway, I have some good news."**

Samus was thankful he couldn't see her rolling her eyes. **"Now that the network is own, I can access the file I mentioned previously. But first, I was able to download data for the Wave Beam and Gravity Suit upgrades." **Samus felt a surge of power as her abilities returned. Adam continued, **"I'm afraid we have some bad news too. I just decrypted a document. It is a communication between General Graeme and high ranking Space Pirates. It mentions a Metroid Project."**

TO BE CONTINUED.


	6. Chapter 5: Reactor Exterior

Author's note: Sorry about the long wait, had exams and stuff. The remaining updates (There will be 12 chapters in total) should come out in a more brisk manner.

"Whoah, looks like the A.I. just went off line." said one of the Federation agents. General Graeme suddenly felt a wave of panic come over him. This had to be her fault. Already he began to wonder how much Samus and her rogue computer had discovered by now. The plans were stored in the A.I. for a reason, to prevent what was happening now. Because if the rest of the Federation was aware of what Graeme was doing, he would spend the rest of his life in a prison cell.

Graeme took a second to compose himself. This could easily result in his worst case scenario, and he had to stay ahead of Samus and the Federation to come out on top. He got up, adjusted his suit, and began walking toward the door. He approached one of the troops. He quickly grabbed the soldier's stun pistol from his holster and shot him. Wicket and the rest of the officers in the room stood up in shock. Graeme promptly shot them all one by one and began running.

He sped down the halls, thinking to himself furiously. He had to put some distance between himself and the officers. Once they regained consciousness, the manhunt would be after him instead of Samus. But that didn't matter. As long as they stayed on the colony, they would all be dead within the next few hours.

Samus dove into the shining blue water. Technically it was actually a chemically engineered coolant designed to keep the reactor from overheating, but it felt just like the waters of Maridia she swam in as a child. She had reached the exterior region of the reactor, which consisted of a series of pipes and tanks which transported the coolant throughout the facility.

She came up and started running down a corridor, the sounds of dripping sand splashing creating a soothing melody. Samus saw two familiar silhouettes. A pair of Space Pirate troopers patrolled the area. The lobster-like creatures were already inside the colony. Samus took a deep breath and rushed in, shooting the two Pirates.

**More of them will surely be coming soon. We should be careful."** said Adam.

Samus entered another pool and rolled through a pipe, leading her closer to the colony. She had to warn its inhabitants of the danger they were in. She came out of the pipe and reassumed her normal shape. Large vats of the coolant had catwalks sprawling above them for the workers. Within seconds, she saw each path was blocked by Pirate Troopers.

Samus got a running start, dodging fire from all sides. She gunned down most of the troops with a strafing maneuver, leaving only two left. The both rushed at her, snapping their claws angrily. Samus swung over a railing and held on under the catwalk. She fired her wave beat through the metal platform, killing the Pirates.

She saw a hovercraft emerge from the liquid below, sporting rapid fire artillery. It was piloted by a Space Pirate Commander. She got back onto the catwalk, and began running back and forth, avoiding the massive bullets fired in rapid succession. She fired a fully charged Ice Beam, followed by a salvo of missiles. Neither of them had any effect.

The Pirate Commander laughed to himself for a moment, and then continued firing. _This is going to be a bit tricky,_ Samus thought.

She switched to her Wave Beam. The shots passed straight through the Machined armor, roasting the cockpit inside. The hovercraft spun out of control, crashing into a wall. It spewed flame and rubble in every direction, but the Commander jumped out before the crash. Brandishing a sword, he rushed at the bounty hunter. Samus feinted, rolling underneath him as he kept running.

He turned around for a second attack, but Samus was prepared. She switched to her Ice Beam, Freezing him solid with a few carefully aimed shots. She got up and fired a missile, shattering the frozen Commander like glass. Before Samus left the room, she picked up a cylindrical object. It was a power cell for the hovercraft's guns. She drained it with her palm spikes and downloaded a new weapon called the Tactical Beam. It was slightly weaker than the Power Beam, but was capable of rapid fire and a quick burst after charging shortly.

As she continued through the watery passageways, Adam told her to stop.

"**You need some morph ball enhancements to proceed." **said Adam, referencing the elaborate ducts she would have to navigate. **"Fortunately, I can download them now that the A.I. has been deactivated, using Espan XI's network."**

After a few moments, Samus had regained the Spider and Boost Ball abilities. She climbed and sped through the labyrinthine system of ducts. Curves, loops, and sheer drops, many of which were underwater, did nothing to slow her down.

"**We have now reached the edge of the reactor complex." **said Adam, as Samus came out. He continued, **"Would you mind answering a question for me?"**

Samus was a bit taken aback at this. She thought, _I'm in a bit of a hurry; galactic safety is at stake here. This is why I normally travel alone._ But she listened to him anyway.

"**I have been rediscovering some of my… predecessor's memories."** explained Adam. **"One phrase Adam Malkovich kept thinking was 'No good deed goes unpunished.' What is the meaning of this statement?"**

Samus sighed. Unintended consequences, even in the face of success, had always bothered the original Adam. Samus always thought his guilt was part of the reason they had drifted apart. Although a brilliant strategist, Adam Malkovich was not very good at dealing with emotional issues.

Samus explained, "Sometimes, even in our greatest accomplishments, things go wrong. For example, this entire mess, and the B.S.L. incident, and the destruction of Zebes, can be linked to one event: I saved the infant Metroid. Adam was never able to really deal with this concept when his missions did not go perfectly."

Although Adam didn't seem too reassured, Samus felt a little better. Being able to talk to Adam about things that weren't trying to kill her was nice, as was being able to discuss her feelings with someone she trusted. Samus entered a hallway that was completely flooded. She was surprised to discover that, not only did her suit allow her to pass through it unhindered, but the new model actually allowed her to hover or fly upwards while submerged. She was actually more maneuverable underwater than on land.

She entered a large atrium, with a giant pool in the center and a dock in the center of the pool. Samus leapt over the pool and stopped on the dock. The outskirts of the dock were crunched and shattered from below, leaving only a small area for Samus to stand on. Enormous serpentine heads emerged from the pool, surrounding Samus on all sides.

The serpents began howling angrily, and began their attack. Several would lunge at Samus at once, forcing her to deflect them with gunfire or dodge. One head struck down in the center of the dock, forcing Samus to one side. As she shot at it, a second serpent struck her from behind, launching her off the dock and into the depths below.

As Samus became submerged, the Gravity Suit activated immediately, allowing her to float up. Now she was able to see the true form of her attacker. It was not a group of organisms, but one, single creature, no doubt a Space Pirate experiment. The heads were in fact tentacles, connected to a single, pulpy body with a pulsating eye at the center.

The Leviathan began swimming towards Samus, its tendrils pulsing with anticipation. Samus was at a significant disadvantage. The Leviathan was more maneuverable than she was, and many of her weapons were less effective. The Ice beam acted on the liquid before it reached her target, and her Missiles moved slowly. The Leviathan seemed to laugh at her attack and swung its tentacles at her, knocking her into the wall.

Samus shook her head, trying to gather her thoughts. She couldn't take another it like that. She knew the creature's eye was vulnerable, but she none of her weapons seemed to hurt it. Then a crazy idea entered her head. She rolled along the walls of the tank using her Spider Ball ability, until she had built up some momentum and was directly in front of the creature. She bounced off the wall and activated the Boost Ball, zooming right into the mammoth eyeball. She struck with tremendous impacts, causing the creature to rupture and explode.

Samus floated up out of the pool and left the room. She exited the reactor complex, making her way to the public sector of the colony. She was done running away. She was ready to fight the Pirates and the Federation, but would do so in their territory, on their terms. That would make her victory all the more satisfying. She had been through a particularly stressful ordeal today, and was ready to ruin somebody else's day.

To Be Continued.


	7. Chapter 6: The Public Sector

Author's Note: We're getting into the home stretch here. Up until now, the story has played out like most Metroid games, but here it starts to branch out a bit. 

Samus entered a calm and serene lobby. She was done with all the hazardous locations filled with vicious creatures and Space Pirate forces. For the first time in days since the expedition on SR388 she was back in a place that could be deemed "civilization". Finally, she would be able to warn the citizens and clear her name. There was just one problem. The place was empty.

The bounty hunter tried to not let this bother her. Maybe they were staying in their homes because of the "dangerous fugitive". Maybe someone in the Federation had gotten word of the Pirate incursion. Maybe there was a really good holoball game on. While looking for civilians, she decided to take some time to admire the state of the art colony.

The Espan XI colony was a "snow globe" model facility. This referred to the giant protective shield that encapsulated the city, protecting it from hazardous weather. Not that it needed this, as the sun had been shining brightly all day. Samus noticed a billboard for the new zoological park, which touted alien exhibits, as well as prehistoric earth creatures revived by genetic scientists. Samus couldn't help but think about attending if and when this whole mess was over.

As Samus walked across a glass bridge between skyscrapers, she felt a haunting chill come over her. She surveyed the city and saw no pedestrians or traffic, nobody moving about. It was like something drained the life from the entire colony. As she entered the next building, she continued looking around, and saw something that made her blood run cold.

Lying on the ground were the corpses of some of the colonists, turned gray and stringy. They had been reduced to husks, their very lives drained from them like juice from an orange. Only one thing could have done this.

Metroids.

Somehow they were loose in the colony. Samus asked herself, _How is this possible? Did the Space Pirates Really do this? _This was her worst nightmare, which she had sacrificed so much to prevent. Metroids were now loose in a populated area. The only thing she could do now was keep things from getting worse.

She continued through the building, her combat senses on their highest alert. She walked down a service staircase and heard that wretched shriek. She looked down and saw a quartet of Metroids hovering at the bottom. As they became aware of her, they clicked their spiky mandibles in anticipation and rose up after her.

She jumped up off the rail and fired a slew of Ice Beam blasts at the creatures. As she passed between their freezing bodies she slid down a rail to the bottom, still firing as she went. Once she stopped, she looked up and saw they were frozen. She launched a salvo of Missiles, shattering the Metroids into a sparkling mist.

She opened the hatch to continue onwards, and another Metroid appeared out of nowhere, already latching on to her. Becoming weaker by the second, she quickly entered morph ball and bombed the spiny jellyfish. Not wasting a second, Samus quickly froze and destroyed the Metroid. Then she slumped against a wall and took a second to catch her breath.

As she lied there resting, Samus heard footsteps approaching. She looked up and saw her fellow bounty hunter, Algor. But something was slightly… off about him. He was standing unnaturally straight, and his steps were more mechanical. A green glow shined from behind his visor. He spoke in a lower, synthesized voice, **"Sleeping on the job is only going to make my job easier."**

Samus asked, "How could you Algor? How could you possibly be involved in this massacre?"

The voice answered, **"I'm not really Algor. I'm a computer program put directly into his cerebral cortex, and currently control his actions. I support this because I'm programmed to. Also, I had a bit of a conflict with the Galactic Federation in my previous life."**

As he finished speaking, Samus quickly got up and began opening fire on him. Algor shot out a Grappling Beam and dragged Samus towards him. She grabbed his arm and pierced his armor with her palm spikes. He threw her off before she could drain all of his energy, but she already drained enough to acquire her own Grappling Beam. The shot it up at the ceiling and swung into Algor, launching both him and herself out of the window. As they both fell along the skyscraper, she fired with her tactical beam, and he returned with his plasma pistols. The rapid fire shots struck the windows around them, and broken glass obscured their visions.

Samus rolled into the morph ball, weaving to and fro to avoid Algor's fire. As she got lose to him, she Boosted horizontally, speeding into him and across the city. They both crashed through the window of another building, and found themselves in an abandoned office. Samus got up and took a second for the nausea of her little stunt to wear off. She was interrupted by plasma blasts from her opponent.

Samus ran into Algor and delivered a roundhouse kick to his face. She kept up the offensive, delivering further kicks and punches before he had time to react. He slid across the floor and onto a balcony from the impact of her blows.

He looked up and said, **"Aren't you persistent? But even that somewhat pathetic drive those inane Chozo infused you with won't be able to stop my cohorts. The Federation will pay for what it did to me and my previous endeavors." **He then uttered a stream of profanities in a variety of alien languages. Samus found it somewhat unsettling, yet slightly amusing, to hear such caustic words from such an emotionless voice. Whoever the program was based on, the programmers hadn't done him justice.

Samus slapped the hunter with her Arm Cannon, which sent him flying over the edge of the balcony. She watched him fall, and saw him grapple along the side of the building and disappear into the streets below. There was no way she could follow him, so she continued her search for survivors.

She walked through the abandoned city. She encountered an Alpha Metroid, protected by an armored carapace. She was easily able to destroy it by shooting its exposed underside, but the fact that they were evolving did not bode well. Shortly thereafter, she found a heavily demolished storefront littered with Metroid corpses.

"**What could have done this?"** asked Adam.

Samus didn't have any guesses, but recognized the perpetrator was a force to be reckoned with. The damage actually looked like something she would do; the Metroids had been frozen and detonated by this individual. Although she was glad to have a potential ally, the mystery to their identity was slightly unsettling.

Samus filed this under "Creepy stuff to worry about later" in her head and moved further throughout the city. Soon she found herself in a long heard a loud, rhythmic banging sound. Suddenly, the wall shattered to her right and a hulking behemoth emerged. The huge, drooling figure was an Omega Metroid. She felt a shudder of dread move through her body. She couldn't do it. She had barely beaten the one on B.S.L., and that had been at the height of her power. She was completely drained after her skirmish with Algor, and didn't stand a chance.

A series of armor-clad figures emerged from behind her, brandishing Ice Beams and assault rifles. She recognized them as Federation troopers. For the first time today, she was happy to see them. They immediately grabbed the attention of the Omega Metroid, who began charging at them. They opened fire, and it succumbed to the onslaught, collapsing on the ground.

One of the troops walked up to Samus. He removed his helmet, revealing himself to be colonel Wicket. He reached out his hand to Samus, helping her up. He said, "I don't know if you're aware of this, but things have been going pretty terribly. We'll take any help we can get. The Federation is prepared to issue a pardon, but you have to do us a favor."

Samus couldn't help but be suspicious. She asked, "What do I have to do?"

Wicket replied, "What you do best. General Graeme has turned traitor. We want you to bring him in."

To Be Continued

Author's Note: Than you sooooooooooooooooo much to everyone who wrote a review, or added me to their favorites, or set up a story alert, or liked on my tumblr. It means so much to me. Anyway, come back next time (hopefully tomorrow!) when Samus hunts a bounty for the first time in like, ever. 


	8. Chapter 7: The Train Network

Author's Note: This is a fairly straightforward chapter. I usually find recommended listening for fan fiction to be somewhat pretentious, but I do think this would go well with the Serris/Yakuza theme from Metroid Fusion, or any remixes you can find. Try YouTube or something.

"**Are you sure this is a good idea?" **asked Adam.

"What makes you think it wouldn't be?" asked Samus in return.

"**The Galactic Federation has repeatedly proven itself untrustworthy, and it is clear a high ranking officer was involved in the outbreak. How do we know it was Graeme?" **said Adam.

Samus had already thought about this. "I know Graeme. He has been responsible for some of the most stressful events I've had to live through recently. I have also seen some of his psyche evaluations which have been… less than stellar. Trust me, if anyone did this, it would be him."

The Federation soldiers had been kind enough to supply Samus with a Stealth suit, a dark green battle suit that would allow her to sneak past Space Pirate sensors. According to footage from security cameras before the Metroids had taken them offline, Graeme and the Space Pirates were congregating in the public train hub. Efforts to navigate the tunnels and locate them had proven unsuccessful.

Samus stated walking through the labyrinthine tunnels. They stretched to all parts of the colony, and one elevated track circled the outside. Samus had guessed that her prey would be hiding near the outskirts, and stated to follow a trial in that direction. She could hear every step she took echo through the darkness, and a chill came over her. She almost felt like another presence was down there with her.

She followed a distant ball of light, growing larger as she came near to it. She came close to the end of a tunnel, the gateway to the outside of the colony. She heard the scuttling of Space Pirates and saw them moving large containers. She caught a glimpse of Graeme giving the Pirates orders. He was no longer wearing his General's suit but black army fatigues and body armor. Samus briefly remembered some of his impressive military exploits before he became involved in the business of insane science experiments. For the first time she became slightly worried about her ability to take him down.

Samus decided to get a closer look. The trains operated like an inverse monorail; trains were suspended underneath a rail that was shortly below the ceiling of the tunnel, similar to the transport system in Skytown. She Grappled up onto one of these rails and crawled along the top, obscured from the view of her opponents. She saw that they were loading one of the trains with weapons and cargo. One particularly large object was being loaded into the front car.

"**That appears to be a tripod mounted, long range missile." **whispered Adam.

"If they ride the train along the outside rail they fire it at the colony." said Samus.

"**And if they hit the reactor, a chain reaction could destroy the whole colony, wiping evidence of what happened here. Then the conspiracy could continue its plans unabated."**

Samus knew what she had to do, and acted quickly. She grabbed a Space Pirate from beneath her with her Grappling Beam, unnoticed by the other Pirates. To her surprise, she was able to drain his energy like a Metroid with the Beam, which connected to the spikes from her hand. He fell to the ground with a thud, revealing her presence. She swung down from the rail, already firing her tactical beam in all directions. While the Space Pirates reeling from surprise and confusion, Samus fired her missiles, taking each of them out individually. She looked up to find survivors, and was greeted by a hail of bullets.

Samus fell flat on her back, reeling from the concussive pain of bullets hitting her armor. Graeme walked toward her, brandishing an assault rifle. He stepped on her right arm, pressing her Arm Cannon to the ground. He pressed the end of his weapon right against her forehead.

"I have to say, your constant attempts to impede my progress confuses me. You of all people should know about the state of the galaxy. You should understand why my allies are necessary." he said with indignation.

Samus replied, "What are you talking about? How could you possibly justify the horror you've unleashed on those colonists?"

Graeme chuckled to himself. "They, like all the citizens of this pathetic Federation, have grown lazy and ignorant. Ever since the death of Mother Brain and the extinction of the Metroids, people have lost their drive. They have forgotten the sense of duty that came from the fear the Pirates inflicted. If society is ever going to get back on its feet, they need some motivation. The Pirates are going to give it to them and the events on this colony will start a movement for change." As he gave his monologue, he seemed to get angrier and bitterer with every word.

Samus had dealt with her fair of terrorists, serial killers, and other psychotic murderers, all of whom gave her some attempt to justify their actions before she brought them in. Although the general's crimes were unique, he revealed himself to be no different from any other bounty she brought in. More confident in this realization, Samus swung her legs out, tripping Graeme.

She ran for cover as Graeme opened fire again. He ran to the front car of the train, which began to pull out. Samus ran after the train, but the tunnel quickly came to an end. She jumped up and fired her grappling beam from her palm, latching on to the last car. She was pulled off her feet as the Train dragged her out of the tunnels and into the open air. She could see the trees in the jungle zoom past her, hundreds of feet below.

Samus climbed through the back window. Every second that passed by, the train came closer to the target and Graeme would launch it. She started making her way to the front, but Graeme noticed her. He began firing through the windows of the doors between the cars. Samus took cover behind a door. As Graeme stopped to reload, she curled into Ball form and bounced through the door using a Bomb blast.

She rolled closer to the front of the train while Graeme tried to find her. When he did, he started shooting again, and Samus returned fire. He ducked behind the front door, where Samus couldn't see him. Samus switched to her wave beam, and fired a quick blast. It passed through the door and stunned Graeme. Samus used this opportunity to run to the front car. When she reached it, Graeme was nowhere in sight.

The general leapt from behind her, slapping her with the side of his gun. Samus punched him back, but he grabbed her arm and through her to the floor, she jumped up and kicked him in the chin, midair. She swung at him with her cannon, but he dodged it and kicked her in the stomach, sending her against the wall. Samus saw the missile and kicked the end of it. It spun around on its pivot and hit Graeme, pressing him against the control dashboard.

Samus fired a shot with the Ice Beam at the missile, which froze in place and trapped the General. The general gave her a look of pure malice. "How could I expect you to understand?" he spat. "You're not even fully human anymore. Those predator instincts from your… vaccine must be overriding your common sense. I knew that procedure was a bad idea, but the damn doctors didn't listen. They never do."

Samus got closer to him, bringing their faces inches apart. She said, with equal disdain, "I haven't been fully human for years. And if the Metroid DNA is making me more of a predator, you must be a real piece of work, because I can still see what a monster you are."

She walked out of the car and popped her head out of the window of the following car. She shot off the restraint bold holding the front car up, causing it to fall. It sped past he train in a diagonal arc down into the jungle below. It exploded into a gigantic fireball, scorching nearby trees. Samus turned on her communicator to inform Wicket that she was successful. "I killed your boss. How big a medal do you want to give me?"

Wicket ignored the joke. He said in his quiet, monotone voice, "Thank you. Expect a full pardon in a few days. By the way, I want to congratulate you on raiding that Space Pirate hideout. You killed about a dozen of those oversized lobsters."

Samus was confused. "I never raided a hideout. I spent the whole time hunting Graeme." Her mysterious ally was helping her again. Feeling slightly uncomfortable, Samus rode the train back into the colony. She felt like she was being watched, like a giant eye was following her every move. She didn't know that her watcher was none other than the extradimensional spirit Phantoon.

To Be Continued.

Author's Note: Tune in next time, where the story takes a slightly different direction. And in response to ARandomDay's question, I had to introduce Graeme as a traitor early because he died in the next few chapters. Anyway, next time Samus does some Ghostbustin'!


	9. Chapter 8: The Darkness

Author's Note: Continuing with the recommended music, I suggest Nightmare's theme from Fusion (or any remixes) for the majority of this chapter. Also, there is a brief cameo by Ridley. I couldn't help but imagine him with slowbeef's Jersey accent, so there is no reason you shouldn't either.

As Samus rode the train back into the colony, she heard a loud series of explosions. A pang of panic swept through her. She checked her communicator, hoping for an explanation from Wicket.

"What was that noise?" she asked, trying to sound calm and collected. She hadn't gone to all this trouble to protect the surviving colonists for them to die while she was gone.

Wicket answered, "A Space Pirate Frigate has begun laying siege to us. We think it was hiding inside the Chozo Ruins, were we suspect they obtained the Metroid genes."

"Hold tight, I'll be there in a second." answered Samus. This day kept getting worse and worse. The train came to a stop on the outskirts of the colony, so Samus started running through the tunnels to save time. Once again, she felt a chill come over her. As she walked through, the passageways started to blend together.

'Hey Adam, do you have anything on the map? This is really difficult to navigate, and navigation seems to be your specialty." she asked. Adam didn't respond. She checked her communicator. It was buzzing rhythmically, but didn't seem to do anything else. Samus was really starting to get worried.

She ran down the halls, which seemed to stretch on forever. She took a second to recollect herself, and found she was back exactly where she started. She had been running for what felt like an hour, but her surroundings still looked identical to when she had started. Shimmering lights began to emerge from the darkness.

Samus saw ghostly figures moving towards her, like grey, melting faces glued together with no body. Suddenly thing stated to feel a bit more familiar. This was just like the Wrecked Ship back on Zebes. She started shooting at the apparitions, switching between her Ice and Wave Beam. The Ice Beam trapped them by freezing the air around them and the Wave Beam was able to harm them.

After they seemed to stop coming, Samus took a more relaxed posture. "Alright, I know you're out there. Why don't you come and get me, Phantoon?" she asked, calling out the Pirate Lord. After a few seconds, a greenish, squid-like figure shimmered into existence. It opened its toothy mouth to reveal a giant yellow eyeball.

Samus leapt into action immediately, concentrating her fire on the eye. It responded with a wave of blue fireballs, which Samus carefully dodged. The Spirit fired a second wave in the direction she dodged in, always trying to get ahead of her. After dodging several times, Samus was able to see that the fireballs were actually glowing blue eyeballs, which always seemed to stare at her. Just when she thought she had figured out a pattern to the attacks, it swung at her with its tentacles, sweeping her of her feet.

Samus quickly got up as a second tentacle came slamming down, just avoiding being crushed. She started firing at its eye, waiting for periods between its attacks. Phantoon was one of the more formidable Space pirate Lords, but she felt he was one of the more predictable. She started to get into a groove throughout the battle, easily hitting it more times than she was hit. Her first two encounters with the creature had been fairly straightforward, and felt this battle would be easier. Phantoon then proved her wrong.

It fired a stream of pure darkness from its eye, which engulfed Samus. As the onslaught faded away, she found herself in a sunny field. She quickly recognized it as her home planet, K-2l. She saw the smoke and fire in the distance. This was the day the Pirates had attacked, the day her family died. She saw her three year old self walking nervously through the field, apparently unaware of Samus' presence. The girl walked up to the thin, bony figure of Ridley, who was watching the devastation from a hill.

"H-hello." stammered the girl. As Samus watched, she was dumbfounded by both her younger self's bravery and naivety. So was Ridley, who was confused, but began grinning as sadistic possibilities opened themselves. "Would you l-l-like to be m-my friend?" asked the little girl. Ridley smiled in cruel delight.

"Unfortunately not little girl But it would be rude not to ask your name. I'm Ridley." said the Space dragon in the most insincere voice possible."

"I'm Samus Aran. Why can't we be friends?" asked the little girl.

Ridley replied, "Because I have to kill every little cockroach on this scrap of a planet, and that includes you!" He opened his maw, revealing his sharp, crooked teeth, and let loose a blast of fire. Samus' mother swooped on at the last second, throwing her out of the way, as fire engulfed everything in sight.

When the flames cleared, Samus found herself in an apartment building at the center of a city. She instantly recognized the building, and remembered the last time she had been here. A feeling of dread crept into her as she realized what she would be reliving again. She saw a slightly younger version of herself in her police uniform with another officer. They were sneaking up on a madman who had trapped his coworkers in an office with a bomb. He was negotiating with the police via online communicators, and didn't know they had found him.

Samus watched as her younger self and the other officer snuck into the apartment, listening as the man ranted about the government and his mother to the police. They pulled out their stun pistols, preparing to fire. But the psych heard them and pulled out his weapon and fired. He shot the other officer, but Samus managed to hit him squarely in the chest. She had to ignore her partner rushed to the madman, making sure he didn't get up. She saw in the palm of his hand he had already pushed the detonator. The whole operation had been a waste, she had lost her partner, and the target had set off the bomb. There was nothing she could do.

As the scene melted away again, Samus found herself alone in a open room. She didn't see her past self, but recognized her location as Sector Zero of the BOTTLE SHIP. She was in her Zero Suit, and Adam Malkovich was standing near her. She immediately recognized this memory as when he sacrificed himself. To her surprise, the memory didn't play out as it originally had.

Adam walked up to her and said, "This is really all your fault. You could have stopped Ridley, or made sure the Infant's DNA was secure, or blown up the ship. But here we are, with me paying for your mistakes." His voice was strange, as its tone seemed to modulate randomly. He continued, "The Chozo granted you the power to protect the galaxy. But no matter what you do, or how hard you try, it will never end and you will never win. Just give up."

The walls around them began to come apart, revealing a black void. She could see Nightmare, Dark Samus, the Metroid Queen, Emperor Ing, and Mother Brain watching her. Adam said, "Even though you've beaten impossible foes like these guys, and escaped with your life, there is always a cost. You lost your parents, those hostages, the Chozo, and now me. Shouldn't you just back down?"

"No." replied Samus. "Even though there are consequences, I always do what's right, and I always make things better. Your pathetic psychological attacks won't work on me, Phantoon." As she said this, her Power Suit materialized around her. Adam roared with fury, but Samus Shot him directly in the chest without even flinching. The room began to melt and evaporate around them.

Samus saw she had returned to the tunnels. Phantoon was writhing in pain, lashing out like a cornered cobra with his tentacles. But He had no effect on Samus, who fired one last salvo of missiles at the Spirit, hitting its mammoth eye. It wriggled and spasmed, eventually disappearing in a flash of light. Samus activated her communicator, which was functioning again.

She called Wicket, who sounded very exhausted. "I would like to request payment for the bounty on a high ranking Pirate leader, Phantoon." she said.

"Phantoon's here?" asked Wicket.

"Not anymore." answered Samus. "Anyway, how's your day going?" She continued humorously.

Wicket said, "Quite frankly it's a bit of a war zone. We need all the help we can get. But before you come over here, there's something else you can help with. Our 'helpful friend' has turned on us, attacking a security platoon. Is there any chance you could catch him?"

"**I have detected erratic patterns in the Zoological Sector." **said Adam. **"We should start there."**

"I always wanted to go there." said Samus as she hung up on Wicket.

"**Then we should get going." **said Adam. In a seemingly less monotone voice than usual, he asked, **"Are you okay Samus? You seem to have suffered a very emotion experience."**

"Never been better." she replied.

To Be Continued.

Author's Note: That was a little bit long, but  
>I felt it was important to tell. It was originally going to be a part of the last chapter, but I decided it needed its own entry, and it turns out I was right.<span>


	10. Chapter 9: The Zoological Park

Author's Note: This chapter originated in a dream I had as a kid, so let me know if it's too ridiculous, and I'll tone it down. Anyway, recommended listening this time is Green Brinstar, preferably the Shinesparker's remix.

Samus carefully made her way back through the colony, always watching her back for more Metroids. If they got her by surprise, there would be almost no chance of survival. She heard the sounds of battle far away. The sots and explosions triggered an instinctive response, but she did her best to suppress it. Despite how much she wanted to help stop the siege she had other matters to tend to. She asked herself, _Is this really the most valuable use of my time? _But no, despite how much she wanted to kill Pirates, whatever was lurking through the colony was incredibly dangerous and unpredictable. She was the only one who could stop it.

She reached the edge of the Zoological Park. One of the observation windows had been shattered, giving a better view of the artificial prehistoric landscape. Her "friend" had already been here. She stepped into the exhibit, taking a moment to let the atmosphere sink in. One of her few memories from K-2L was a holobook about prehistoric earth life, which fascinated her, but was forgotten when she was adopted by the Chozo. The strange world and the creatures in that holobook came back to her memory in each of her many journeys.

She heard some bushes rattle, and aimed her Arm Cannon, not wanting to be ambushed. She saw small, bird-like reptiles scurry through them, moving away from her. Then she heard thunderous footsteps behind her. She looked up and saw a creature anyone in the galaxy knew the name of, even though it had died out on Earth eons ago. The Tyrannosaurus Rex looked at her, roared, and charged.

Samus tried to fire a few shots at it, but it moved to fast and was too powerful. The artificial walls that surrounded the exhibit left her no room to maneuver. She had no choice but to run. As she sped through the jungle, the dinosaur got closer and closer. It snapped its enormous maw at her, just barely missing. Samus saw the edge of the exhibit before her, trapping her between rock and a hard place.

She saw a small vent shaft on one of the walls, which led further through the zoo complex. Samus rolled into the Morph Ball, curling around the tyrannosaur's footsteps. Narrowly avoiding being crushed, Samus blasted of the grate and rolled inside. She wasn't safe for long, as the dinosaur started ramming the wall with its head, threatening to burst through.

She crawled up the shaft using the Spider function, which zig-zagged along the outer walls of the exhibits. The tyrannosaur could see Samus through the grates and still tried to get too her. She was at about eye level with the massive saurian. It slammed its head into the grates, demolishing the wall behind her. She boosted away from it, but it chased her, smashing through the wall as she barely rolled ahead of it. Finally she reached the end of the exhibit and entered a special area for the zookeepers.

As she rolled out, she saw massive cages and empty food containers. She walked further down the halls between the exhibits, and saw ballistics marks against the walls. Her prey had been through here. She followed a trail into one of the other exhibits. She continued tracking the intruder. Suddenly, a feathered form leapt out of the bushed at her.

The thin clawed dinosaur leapt on to her, forcing Samus to shake him off. Then two others blindsided her, knocking her against a tree. She fired off several blasts with her Ice Beam, not wanting to kill the creatures if she didn't have to. One of them zoomed past her shots, to quickly for her to hit him. Samus fired several shots onto the ground in front of the raptor, causing it to slip and crash into a tree. Samus fired another shot that froze him solid.

Samus followed the trail again into a larger area, filled with long-necked dinosaurs. She looked up and saw an observatory window that the intruder had exited through. Unfortunately, it was too high for Samus to reach. For a moment she felt a pang of disappointment and irritation. Then she got an idea.

She leapt up into the air, and swung on a tree branch using her Grapple Beam. She landed on the back of one of the gigantic dinosaurs. Despite the creature's mellow moans of protest, Samus ran onto its outstretched neck. The dinosaur flung her off, soaring above the ground. She used the Screw Attack to push herself through the window.

"**That was a very impressive maneuver, Samus." **said Adam. **"But since it is unlikely that our adversary did the same, it must be a being of incredible power and agility to reach this height."**

_Killjoy,_ Samus thought. _But I have to admit he has a point._ Samus had grown to hate it when Adam was right. It usually meant she would have to survive a ridiculous and dangerous scenario. She started scanning around, but the trail had gone cold. She carefully made her way through the observation area, seeing the various exhibits. They seemed unaffected by the Metroids or the intruder.

Samus heard a dripping sound, and went to investigate. She followed it to the source, only to find it was simply water dripping from a overhead pipe. Closer inspection revealed the pipe had been intentionally broken. A sharp, excruciating burst of cold pain shot through the right side of Samus body. Her shoulder and Arm Cannon were caked in frost and unable to move. Samus spun her head to see her attacker. A figure clad in orange armor with white eyes that had no pupils looked back. It was the SA-X.

Samus wondered for a moment how her X-parasite clone could be here. But this gave way to a more pressing issue. The SA-X was preparing to fire a Super Missile, which Samus had no way of dodging. Samus reached out her right hand, firing a Grapple Beam from the palm which struck the SA-X and started draining it. After a moment, the doppelganger pulled itself back. Samus re-acquired the Super Missile and was able to free herself. They both opened fire, and the observatory shook with explosive force.

The SA-X was using the Ice Beam as its primary attack as usual. Samus made sure not to let a single blast hit her, compensating for her disadvantage. Instead she used the Tactical Beam, firing shots wildly in rapid succession. Several shots landed on the SA-X's chest, pushing it back. Although these didn't hurt it much, it was briefly stunned long enough for Samus to let loose a Super Missile. The SA-X disappeared in the explosion for a second, but Samus then saw it being flung down the hall by the blast.

The SA-X got up and stared directly at Samus with its soulless eyes. Its body shimmered for a second, as if it had trouble keeping its form. For a moment it seemed more like an angry animal than a sentient being. It stood up, and fired an unending stream of Ice at Samus. Samus slid under the blast and fired two missiles, further angering her opponent.

The SA-X was growing tired of this. It fired a missile at one of the windows and then turned away from Samus. To the bounty hunter's surprise, it actually started to walk away from her! Samus ran after her at full speed, but a blur of scales smashed into the hallway with tremendous force. The tyrannosaur had returned.

Samus hoped she would be able to get past the dinosaur, but it obstructed her path. The SA-X escaped into the facility. Samus looked up at the tyrannosaur's head, which was poking into the hallway. She leapt up into the air and carved into its face with the Screw Attack. The dinosaur reeled in pain as Samus full into the exhibit.

The dinosaur swung its tail at Samus, which she jumped over. As she was behind it she took the opportunity to fire an Ice Beam at its back. The dinosaur turned towards her and bit down on her. She rolled into the Morph Ball to avoid its teeth and laid a bomb in its mouth. As Samus fell out of the dinosaur's maw, she fired a Super Missile at it. The tyrannosaur looked at Samus as if it decided she wasn't worth it anymore. It walked back into the jungle. Samus heard its thunderous footsteps grow quieter and quieter.

Samus leapt back out of the exhibit and tried to follow the SA-X. The trail had grown cold. She heard a buzzing noise as the Public Information system came online. She looked up at a monitor on the wall and saw the face of Algor. The bounty hunter was still stiff, and a purple glow emanated from his visor.

The intelligence controlling Algor then spoke, **"Attention pitiful survivors of the Espan XI colony. You are no doubt exhausted from your battle to survive. Fear not, you should be able to relax soon." **A Strange digital shriek followed those last words. As best as Samus could tell,, he was laughing.

He continued, **"You will bear witness to an historic day. This will be the first battle in the war by the glorious Space Pirate Armada against the Galactic Federation. The ineffectual and pathetic bureaucrats will be overthrown, and the justice of Anarchy will reign supreme. There is nothing you can do to stop this. Defeat is inevitable. But you can help this momentous revolution. All you have to do is give up, accept your fate, and await death!"**

There was another electronic screech, followed by the words, **"Have a nice day!"**

Samus felt an urgent buzzing on her arm. She activated her communicator and was greeted by an exasperated-sounding Colonel Wicket. He said, "We need your help immediately Samus. Drop what you're doing and come to the Administrative Sector."

Samus said, "But I have identified the saboteur. It is a being of unparalleled power and zero remorse."

Wicket replied, "Maybe it will take out a few of the Pirates. They have started a ground invasion, and we don't have the manpower to stop them."

To Be Continued


	11. Chapter 10: The Administrative Sector

Sorry this one took longer than usual. Anyway, enjoy this chapter, only two more to go. Recommended listening is the Space Pirate theme from Metroid Prime.

Samus found some relaxation from the rhythmic clicking sound her boots made. It echoed throughout the hallway like a metronome. As she reentered the colony, it was drowned out by gunfire and explosions. She looked out a window and observed the city below. The "snow globe" had been shattered, and Space Pirate fighters swarmed the city like a swarm of wasps. Samus felt the building shake, and saw a chunk of rubble zoom past the window, smashing into the ground.

"Adam, what do you scans indicate about the Pirates?" asked Samus.

"**The Frigate is indisposed fending off the colony's defense cannons, so the ground forces and aircraft are doing the real damage. They are passing from building to build, pelting each with a small, but not insignificant, amount of fire." **

Samus said with a sigh, "They're looking for the survivors."

Adam said, "**Correct, they are masking their search with wanton destruction, while at the same time instilling fear in the survivors. Standard procedure for the Pirate armada."**

Samus said, "I was about to say that. How do you know about Space Pirate tactics?"

Adam replied, **"I retained some of the original Adam Malkovich's battle reports with his memories."**

Samus ran toward the Administrative Sector, an enormous skyscraper at the center of the city. As she approached the exterior, she saw a band of Pirates trying to break in through the wall. "Hey, over here! One of the downtown restaurants is having a steamed lobster special!"

The Pirates dropped their tools, looking at her in confusion. She fired a Super Missile, hitting them all at once, before they had a chance to respond. After a moment, Samus heard a soft, high frequency noise coming from their direction. She peered through the smoke with her Cannon raised, only to see a communicator switched on.

The now familiar voice of Algor (or rather, the intelligence inhabiting his boy) screeched at her, **"You're really starting to bug me. Don't you ever quit?"**

Samus responded, "Not as long as the pay stays this great. You're the one who should quit. Compared to Mother Brain, Dark Samus, and even Graeme, you're a bit of a disappointment. I already killed a power-mad A.I. today, who was three times more threatening than you, and not nearly as annoying." She moved closer to the communicator, making sure he could hear her every word.

He replied, **"Oh, that's funny. That's almost as funny as your first interview after stopping the operation on Zebes. Remember, the one where the reporter thought you were a man? I must have watched that thirty times. Just thinking about it makes me want to gag, even though I don't have lungs anymore. Anyway, a bombing run should start in about… two minutes ago. Have fun burning to death."**

Samus kicked the communicator across the floor and walked into the Administrative Sector. People were buzzing around, talking quickly over each other to be heard over the bombing. She came to a gigantic elevator. As she rose to the very top floor, she couldn't help but think about the noises outside.

She asked herself, _what if we can't win? What if the Pirates demolish our defenses? I may not be able to stop them this time. We're outmanned, and I can't fight off a whole battalion._

She stepped out of the elevator and saw the red glow of the sun fill the room. A gaping hole was situated at the center of the ceiling, giving a gorgeous view of the sunset, as well as the purple, whale-shaped Pirate Frigate. Wicket walked up to Samus, stepping past several soldiers and security officers. A bandage covered his right shoulder. He sounded out of breath as he said, "Thank heavens you're hear. We can't outlast the Pirates in a straight siege. That's their specialty."

Samus said, "Well do we have a plan, or should we sit back and enjoy our fiery annihilation like that annoying computer said?"

Wicket seemed to not notice the joke. He said, "If we hold them off a little longer, we can weaken the defenses on the Frigate. If you can sneak in and work your magic, we might have a chance at surviving."

Samus was about to ask how she was supposed to infiltrate the Frigate, when something in the sky caught her attention. A small orange figure was latched on to the wing of one of the Pirate fighters. The fighter spun out of control, crashing into the Frigate. After the explosion cleared, while was visible in the side of the floating behemoth.

Adam said, "**It appears that the SA-X has already entered the ship. Perhaps one enemy can take the other out."**

"Maybe I can take out to birds with one stone." chimed in Samus. There was a humming noise in the air, growing gradually more frequent. Samus saw a large blue sphere of energy fly towards them, and told everyone to duck. A massive explosion shook the whole building.

A Space Pirate Bomber curved towards the structure. The large cannon on its underbelly was still smoking. It fired plasma blasts at the exposed soldiers with thin guns on the tips of the wins. Samus launched Missiles at the Bomber as quickly as she could. She heard gunfire behind her as the Federation forces joined her.

The Bomber weaved back and forth, spinning between the bullets. It launched another blue bomb, which sent a powerful shock wave through the building. Samus was thrown back, and some of her allies went flying past her. She sprung back up on her feet and shot a fully charged blast at the Bombers, wing, causing it to spin into a downward spiral. It headed straight for Samus.

The Bomber flipped onto its back, and the cockpit at the front rotated counterclockwise. The machine now hovered in the room. It resembled a tank more than a plane. It rammed towards Samus, firing wildly as it charged at her. Samus rolled to the side and fired some Missiles as it sped past her.

Wicket got up and grabbed an assault rifle that had been strewn on the floor. He walked up to Samus' side, and began shooting alongside her. The machine fired another energy grenade from its cannon. The blue sphere burned through the air, but slipped between its two targets. It pierced the wall and sped off into the distance.

Wicket used the brief pause in the machine's attack to fire some carefully placed shots at the cockpit. The bullets hit the bottom rim, causing small cracks to appear in the dome. The pilot fired more plasma bursts in retaliation. The bright lights glowed throughout the entire room. Wicket was briefly blinded, allowing a green blur struck him in the chest.

The pilot watched as Wicket was thrown off his feet, and then tumbled to the ground. The pilot then heard a loud thud outside his cockpit. He looked up and the helmet of Samus Aran appeared in front of him. She froze unloaded a Missile into the cockpit at point blank range. As glass shards rained down upon the pilot, Samus grabbed him and threw him out of the ship. He spun out the hole in the wall, and then dropped down to the streets below.

Samus ran to the fallen form of Wicket. She asked, "Are you alright?"

"That's not important right now." he responded, struggling to breathe. "You are the last line of defense. Go show those Pirates why they call you the greatest warrior in the galaxy." He then faded into unconsciousness."

Samus hurried back towards the Bomber and entered the cockpit. One of the wings was damaged, but she wasn't expecting to land it when this was all over. Adam asked her, **"What exactly do you plan to do?"**

She answered, "I'm going to board that ship, fry any Pirate that gets in my way, and then blow the whole thing all the way to Tallon IV. Along the way, I'm going to top Algor, and take out the SA-X once and for all. Nobody is going to stop me this time."

To Be Continued

Author's Note: I would like to thank everyone who has given me feedback so far. You have all been very kind and helpful. I would like to extend a special thanks to Crunchthe Robot, who has been following this from the beginning, and has started uploading a reading of this story on YouTube. Anyway, come back soon, it's not over yet.


	12. Chapter 11: The Pirate Frigate

Author's Note: Whew! Time for the final assault on the Pirate Frigate! I would like to take this opportunity to ask one last time for any feedback, and to extend my thanks to those who have already given it. Anyway, Recommended Listening this time is the classic Brinstar theme, my favorite from the series. I especially recommend an orchestral remix.

The world spun outside of the cockpit. Samus turned and spun her hijacked vehicle like a dancer, flying between the gunfire that filled the air. The purple Frigate rained down streams of energy onto the city, vaporizing whole buildings. The auto defense cannons fought back with missiles and lasers that struck the Frigate like harpoons. Samus heard an incoming transmission to the Bomber from the Frigate.

"**No more games," **said Algor. **"I want you to stop right now."**Samus could almost hear a hint of panic in his monotone voice. Algor continued, **"If you are interested in money, feel free to join us. If you are willing to die or the Federation, I'm willing to oblige. I just wanted to warn you about what could happen if they are left unchecked. Do you really trust them after the B.S.L. experiments? You don't know who I really am yet, but trust me, they shouldn't have brought me back. The conspiracies and genocide and experiments will only get worse. If you stand against us, they will only continue to steal from those with true power and poison the societies they control."**

Samus cleared her throat in irritation. She whispered directly into the microphone, "I may not be the biggest fan of the Federation after what has happened in the last few days, but nothing, and I mean nothing, will ever make me support the Pirates. Ignoring my personal history, they have endangered the whole galaxy, forced planets into slavery, and just recently unleashed bio-weapons in a populated area." She paused for a second to regain her composure. Barely masking the anger in her voice, she said, "I'm going to stop you and put an end to the Pirate way of life once and for all."

"**Come and get me," **replied Algor. He spoke each syllable slowly, as if he was frothing with rage, but still remained emotionless as ever. Samus thought he seemed like he was trapped as a computer, brimming with emotion but unable to show it. Algor spewed as succession of obscenities in a variety of languages, bringing a reluctant smile to Samus' face as she switched off the message.

Samus drove into the gaping wound in the Frigate's hull and landed. The bounty hunter stepped out and readied her weapon. _Any second now, the Pirates are going to swarm me with everything they've got,_ she thought. She sped down the halls, glancing over her back as she did so.

Sure enough, the pattering of her feet against the cold metal for was soon amplified by a numerous series of sounds. Samus could hear the troops coming from all directions. She ran forward, but she didn't plan to escape. Instead, she came into a large, open room, and waited.

Space Pirates stormed in, cutting off all exits. The filled the room with an endless flurry of energy blasts. Samus ran into one corner where she was most protected, and began firing Super Missiles. The massive projectiles flew in all directions, leaving her attackers nowhere to go.

Samus stopped firing when she stopped when she saw no more targets. Certain that more would soon be on the way, she raced towards the inner halls of the ship. She came to a long staircase, with two more guards at the bottom. Samus sprung through the air and stood along the rail, sliding down with incredible velocity. She zooming past their shots and returned fire with the Tactical Beam, striking them both in the chest repeatedly. They were dead before she reached the bottom.

Suddenly, a massive explosion rocked the ship. "What was that?" asked Samus.

"**The Frigate will not be able to resist the defenses from the colony much longer and will soon explode. If the ship goes down, Algor and his associates will surely escape and make it appear that they died in the crash. We must stop them before they have a chance to gather their strength and strike again."**

Samus said, "Alright, where do we think Algor is?"

"**Most likely the control bridge," **answered Adam. He paused for a second, and then said, **"Before you go to the area I have indicated on your map, I would like to address a personal matter. I know our partnership has not always been easy, especially considering my origin, but you have shown great kindness and understanding. Thank you."**

The bounty hunter said, "Know problem. Not like I had much of a choice, right." She tried a more care-fee tone of voice than usual to hide her emotions. She never liked awkward emotional situations. She said, "Do you think we can hold off from anymore personal bonding experiences until after I've stopped the imminent terrorist movement that threatens the entire galaxy?" Adam gave no answer. _Still no sense of humor, _thought Samus.

Samus entered an elevator leading to the control bridge. While ascending, she felt more tremors and heard more thunderous explosions. She didn't have much time. The elevator reached its destination, revealing an amalgam of rubble as the doors slid open. The ceiling of the control bridge had collapsed. Monitors and loose wires sparked as small fires burned in the corners. Samus hopped up onto the top of one of several girders that had fallen, pointing up like pillars. She scanned the room, which had been abandoned except for one armored figure.

Algor looked up at Samus. She got a closer look at the bounty hunter's visor, which glowed green as a stream of holographic symbols and letters swirled inside it.

Algor said, **"I don't have time for any jokes right now, Huntress. This is an historic day, in which the revenge against the Federation takes its first step. I can't have you ruining that."** He aimed his two pistols at Samus.

Just as he was about to pull the triggers, a bright white light entered the room. It struck Algor head on, flinging him across the room. Once he landed, a small layer of white crystal had encircled and immobilized him. Samus looked in the direction of the shot, and saw the orange figure of the SA-X.

The doppelganger looked directly at Samus. Its white, soulless eyes seemed to follow Samus, despite not actually moving. Samus felt sick. The creature's faces remained blank and lifeless as ever as it raised its arm cannon. A constant flurry of white energy filled the room.

Samus sprung off the girder, which became coated with ice behind her. The SA-X barely turned its body to track her with its flood of cold energy. Samus was already feeling sluggish from the cold air in the room. If the SA-X were to hit her, she had no chance of escaping.

She remembered the Wave Beam was the only weapon that had proved remotely effective against the SA-X, so she started charging the purple weapon. Once fired, the violet cascades of energy spiraled into the SA-X, knocking it back. It stopped shooting for a split second and grunted in anger. The orange armor began to shift and pulsate as the doppelganger continued bombarding Samus.

The SA-X leapt into the air, surrounded by the glowing aura of the Screw Attack. It rammed down into Samus, before bouncing back up into the air. It stopped atop one of the girders, peering down at Samus. It began to rain cold energy upon the room.

The room was now freezing cold, and the floor was slippery with frost. One sot hot Samus in her left arm, immobilizing it and stopping her in her tracks. The SA-X aimed its cannon, neither glee nor remorse showing through its visor. The ice around Samus hand shattered as a Grapple Beam discharged from her palm. The lightning rope latched onto the ceiling and pulled the bounty hunter off her feet. She swung through the air and slammed into the SA-X. It groaned in displeasure as she knocked it off its perch.

Samus dropped down onto the fiend as it struggled to get up, kicking it in the helmet. It swung its knee into her abdomen and the punched her across the visor. Samus recoiled from the pain, her vision now resembling a kaleidoscope. She fired the Wave Beam in all directions, praying she could hit it.

As her vision recalibrated, Samus saw the SA-X had indeed been struck, and was now standing still in the center of the room. Its armor began to expand and stretch as the creature doubled in size. Its helmet ballooned out and separated into a dozen tiny eyes perched above one glass glare. The legs snaked apart and split into tendrils that acted as toes. The arms branched into tentacles, the Arm Cannon gutting uselessly from the elbow.

Samus lost her breath from the sheer disgust she felt looking at this abomination. The creature was a sick combination between her and the parasite's first host, a hornoad. However, it was composed of the most hideous traits of both, and was double the size of Samus. The SA-X gave a sick cackle as it hopped around the room. Samus weaved from side to side to avoid being trampled.

After she finally calmed herself, Samus began firing at the frantic creature. Surprisingly, it had noticeably less endurance than the previous form. Samus fired three purple shots at it, and it collapsed onto the ground. The body melted and distorted into a spiky blue sphere. The Core-X floated toward Samus, firing slow ice blasts at Samus. The shots struck the floor, tripping Samus. She slipped as she tried to get up, but when she rose up the Core-X slammed into her. Its spike breached her armor, letting cold air in.

Samus braced herself. She thought, _I may not have much fight left in me, but I didn't come all this way to be stopped by another wretched parasite. _She let loose her Missile, hitting the core right in the eye. The jagged shell crunched and shattered, leaving the gelatinous parasite floating helplessly.

Samus sat on the ground panting. _I didn't think I could beat it, _she thought. She took a few minutes to enjoy the silence, which was cut short by another tremor that shook the ship. She heard a cracking noise, and saw Algor shrugging off his icy restraint. He rolled his head back s his body twitched and jerked. A purple aura emerged from his helmet, composed of digital characters.

It floated into the stranded X, and was absorbed. The parasite pulsated and shimmered into its new form. Red wings with purple highlights stretched out. A purple tail with a dagger-like spike at the end writhed outwards. A skeletal body and a curved, lean head emerged.

"It' good to be back!" shrieked Ridley. The Pirate Lord took a moment to inspect his new body. "You have no idea how good this feels after being cramped inside a hard drive." The dragon then looked at Samus. "How ya' doin' Sammy?" he asked, then cackled to himself. His wings slapped the air, forcing his body upwards.

Samus was petrified. Ridley was back, despite the insurmountable odds and the incredible feats she had accomplished. There was nothing she could do. Algor sprung into action, leaping into the air with his guns blazing. Ridley swung his tail, piercing Algor's armor with the blade at the end. The bounty hunter sped to the ground, landing with a thunderous crash. His lifeless body rolled on the floor, eventually coming to a complete stop.

Ridley laughed and gave a sarcastic salute to Samus and said, "See ya' later, Sammy." He flew off while the ship shook again and rubble tumbled down from the ceiling. Samus just stood there, not knowing what to do, or if what she did mattered anyway.

To Be Continued

Author's Note: Thank you so much for staying with me this far. The next chapter is the last, and I'm ending this story with a bang. 


	13. Final Chapter: The Battle

Well, this is it. The last chapter. Thanks for staying with me this long. For recommended listening, nothing other than the Ridley theme would be appropriate. Honestly, any of the many remixes will do, but I prefer an OCremix called "Dragonfood". Anyway, let's get right to it.

Ridley hadn't felt this happy since his death at the hands of the Queen Metroid. When the Federation scientist had restored his mind, he felt trapped, and only grew to hate the Federation more. He perked up a little bit when they informed him he would be deployed to hunt Samus, and he had gotten a bit of a thrill out of controlling Algor and restoring his forces.

But now, his victory was complete. He was back at the height of his power, and knew exactly how to destroy galactic peace once and for all. He soared through the air, relishing the war-stricken rubble beneath him. Even the sight of his Frigate burning and gradually descending couldn't deter his mood, for he knew Samus was onboard. He flew between the ruined buildings, content that they contained nobody who could pose a threat to him.

"**Samus, what's wrong? Respond!"** a hint of panic was noticeable in Adam's synthetic voice. Samus' breathing was extremely erratic, and her eyes seemed to dash around, never focusing on anything. He pleaded, "**Samus, you have to snap out of it. I know you have a history with Ridley. I know what he did to your family."**

Samus finally spoke up, "It's not just my family. He took the Chozo, the Baby, and even you from me. No matter what I do, no matter how hard I try, he always comes back. He never dies, and never loses anything while taking everything from me." she sighed, and then said, "What's the point in even trying? Even if I win this time, he'll always be back."

Adam thought for a moment. He would have to choose his next words carefully, and emotional discussions were never his strong point. He said, **"I know it seems hopeless Samus. I know you feel like you let the Chozo down, that you let me down. But that couldn't be further from the truth. You have overcome insurmountable odds on many occasions. The casualties that would have resulted if you had been even a fraction less efficient in your missions would be unimaginable. The Chozo had absolute faith in you, which is why they braved extinction to let you lie. That's why the Baby gave itself up for you. That is why the last memory I retained from Adam before his death was of satisfaction.**

Adam continued, **"He knew that even though he wouldn't live to see it, you would save the day and go on to continue to protect the peace throughout the galaxy."**

Samus stood up, shaking the remaining coating of ice from her armor. She asked, "How long do I have until this place goes down?"

"**Less than a minute. It took you two minutes to get in here. Are you ready to face insurmountable odds again?"**

Samus nodded and ran at full speed. The entire ship shook and flames were visible in almost every room. A slight sense of vertigo set in, caused by the fact that the ship was now falling toward the ground. Samus barreled down the halls, jumping over and sliding between the collapsing rubble. At last, the beautiful blue sky of Espan XI was visible.

Unfortunately, Samus had no ship, and nowhere to jump to. She saw Ridley circling in a distance. He hollered, "Where are you going to now, Almighty Huntress?" He cackled to himself. "You're up a creek without a paddle!" Samus stepped back as far as she could, the rolled into the Morph ball.

She rolled along the flaming hull of the ship, building as much momentum as she could. The second she rolled off the edge, she Boosted at full speed. Samus shot through the air like a bullet, speeding directly at Ridley. She hit him directly in the chest, then grinded against his body with a Screw Attack. Ridley roared in pain, and then slapped her off of his body. She fell through the air, and felt a brief moment of panic. But she saw his snakelike, spiked tail and Grappled on to it. She was now flailing through the air wildly, but at least she was attached to something.

Ridley dive bombed into the side of a building. Samus last her grip and was flung through a wall. As she staggered, Ridley crawled out onto the side of the building. He poked his head through a window and spewed fireballs all across the room. Samus walked through the onslaught of flame and fired a Super Missile at his exposed head. Ridley pulled his head back and the projectile careened off into the distance. Samus switched to the wave beam and fired a few shots through the ceiling. They passed through it, the floor above her, and the window before finally striking Ridley.

Ridley was knocked from his perch but recovered, using the momentum to propel himself upwards and towards Samus. With a look of madness and determination on his face, he grabbed her and swept her off into the sky. He tightened her grip and looked her directly in the eye, saying, "Prepare for death, you wretched little…" Samus fired a volley of missiles into his open mouth before he could finish his undoubtedly profanity laced sentence.

Ridley recoiled in rage and brought himself and the Bounty Hunter crashing onto a rooftop. Ridley swung his tail at Samus, tossing her across the roof and towards the edge. The gripped onto the very brim of the roof and brought herself back up. Ridley had taken to the air, and was raining fireballs upon her. Samus endured the flames and emptied her Missiles at the Pirate Lord.

The duel now became a war of attrition. Any semblance of strategy was abandoned as the two, fueled by rage, fired everything they had at each other. The explosions created a smokescreen, and the two warriors were unable to see each other. Ridley said, "Come out, come out, Sammy!" He began stabbing his tail randomly at the ground, trying to skewer his prey. Samus slid out of the way of his tail as it struck at her like a cobra. She grabbed it and pulled Ridley to the ground, ramming his head against the floor.

She charged an Ice Beam and prepared to fire, but he spat out a fireball first. It slammed into Samus, throwing her off the building and into the sky. Samus rolled into Morph Ball and laid several Bombs, using them to slow her descent, eventually landing on a rooftop at the edge of the city. A system of pipes ran across the roof, stretching down across the side of the building. Samus saw a frost-covered warning label read "Caution! Cryo-gel reaches extremely low temperatures and can damage unprotected skin."

Ridley landed on the rooftop with a thud and glared at Samus, his eyes twinkling with insanity. With an exasperated but ecstatic voice he said, "Before I kill you, I want you to know exactly what I plan to do. As I now control the last remaining X parasite, I intend to use their extraordinary capabilities to create a new army. A limitless, expanding array of troops will be under my control, and will be able to take any form they choose."

Samus asked, "What makes you so sure you'll kill me? The scoreboard isn't exactly tipped in your favor"

"Because I don't share your vulnerability to cold," replied Ridley, as he tore open one of the pipes. A glittering silver substance burst forth and coated the rooftop. Samus felt a surge of agony, and was petrified. Ridley showed no signs of slowing down, and stabbed at Samus with his tail. He shrieked, "You've never been anything but a minor nuisance, a persistent setback! Now I'm finally going to be rid of you once and for all!"

A pained smile grew on Samus' face as she said, "Isn't that redundant? If you finally do something, it has to be 'once and for all.' Didn't they teach you anything about grammar?" Ridley howled with anger and slashed her with his claws, then swung a back fist across her face. Samus couldn't take this much longer. She thought, _I'm too cold, too tired, and he's too strong_. The ice was too much, and Ridley seemed completely unfazed. Suddenly, and idea struck Samus.

She started firing wildly with the Tactical Beam. Ridley laughed, as the shot bounced right off him. He said, "What a joke! Is this your final stand, I expected more from the so-called 'greatest Bounty Hunter'. What a disappointment." He perched upon the longest pipe, and touched the end with his claw. If he scratched it, a flood of Cryo-gel would flood towards Samus.

Ridley took his time, relishing the moment. Just as his talon scraped the pipe, Samus fired a Super Missile right under him. A torrent of Cryo-gel struck Ridley, coating his entire body with frost. He was completely immobilized, and the only part of his body still free was his head. Samus walked up to him and aimed her Cannon at his face. Ridley asked, "Do you plan to kill me again? You know I'll just come back."

Samus smiled. "No, I don't. By the power vested in me by the Galactic Federation, I'm placing you under arrest. You have the right to remain silent." She charged the Ice Beam and fired. Ridley's face was completely obscured by ice crystals. Samsu climbed back down and breathed a sigh of relief.

Samus sat in a comfortable lobby as Federation troopers entered the room. _About time, _she thought to herself. A few hours had passed. A special team had begun dropping Ice Bombs, clearing the area of any remaining Metroids. A man in a military suit, brimming with medals, walked up to her. He said, "You did an exemplary job today. We'll handle the rest from here. Any remaining Space Pirates have been arrested and Ridley is being transported to a special cell on the prison ship _Solitude_. "

"Looks like you've done a pretty good job. It's hard to believe that this is the same government that was trying to arrest me for saving the universe from their mess a few hours ago." she said.

"I'm truly sorry about that. Expect a large compensation in the mail soon." replied the soldier.

Samus said, "No problem. Looks like I'll be on my way. Oh wait, before I go, I have something to return. Well, some_one_, I guess. I guess this is goodbye, Adam."

"**Why?" **asked the computerized voice.

"We did pretty well together, and both learned a lot about ourselves, but it's time to part ways. You're needed by the Federation to track down Graeme's conspirators." answered Samus.

"**While you will be busy averting whatever the next big crisis is. I understand. Sayonara, Samus Aran. We made quite a team."**

"We sure did. Thank you, Adam."

**"Would you mind visiting every now and again?"**

"Sure. See you next mission."

The End.

Well, there you have it. Thanks for joining me through this adventure/ungodly mess. I would like to thank everyone who gave me feedback; you were all so kind and helpful. I would also like to thank in advance anyone else who gives their opinion. It will only help future stories. So long and thanks for reading. 


End file.
